Space Seed: What Could Have Been
by RebeccaRoy
Summary: What would have happened if the crew of the Enterprise on finding the Botany Bay had woke up someone else instead of Khan? How could things have been different for all concerned…
1. Chapter 1

Disclaimer:

_Disclaimer:_

_I do not own the characters of Star Trek, I am however borrowing them, no not to make money but for fun and fun only. :)_

_Summary:_

_What would have happened if the crew of the Enterprise on finding the Botany Bay had woke up someone else instead of Kahn? How could things have been different for all concerned…_

Chapter One:

This was the last thing that Captain Kirk expected out here, it was so far from earth that really it should not be here. The small ship (small compared to the _Enterprise_ that is) floated serine in space by the great starship. It had been scanned and it was clear this was a sleeper ship, one of a very few used from earth to bring settlers out to known habitable worlds when warp drive was primitive and it took years to get to places. This ship however did not have warp engines and had been caught in the gravity well of Alpha Ceit Star system. Scans confirmed it was a DY-100, a ship that had been secretly made in the late 1990s in the then secret Eugenics war.

That war had been going on since the end of World War Two, many top Nazi scientists had managed to escape punishment by working for either the Soviets or the Americans. What many had not known until many years after the fall of the Soviet Union is that the Nazis had been playing both sides and creating a "master race" of super solders. History recorded these solders talking over much of the developing world and finally being over come and disappearing. If those men and women were on this ship then captain Kirk had a very real problem according to the ship historian Lt. Marla McGivers.

"There are life signs on that ship Jim." McCoy said leaning on Kirk's chair. "We could use a shuttle to go over."

"Right, we are going to beam over." Kirk said. "Bones, Spock, McGivers with me."

They headed down to the transporter room with McCoy grumbling about having his atoms scattered all over kingdom come. Three security joined them and Scotty beamed them over to the other ship. It looked nearly new, this was due to the fact that the ship having gone nearly light speed roughly three years had passed on the ship while nearly three hundred had passed in real time. The ship was far more advanced than any of them would have expected from this time, a time when the governments of the world denied their people space travel in the light of "national security". Rows of storage containers had one person each, each naked but for a sheet that covered them.

"Most of them survived." McCoy said scanning with his tricorder. "I am amazed that any did."

"What are we looking at?" Kirk asked.

"72 of 80 are still alive." Spock said looking around. "This one is cycling on."

"Cycling on?" Kirk said.

"The computer is advanced enough to know we are on board." Spock said.

It was true, the compartment that held a tall black haired olive skinned man began to warm the man up. Slowly the man was taken out of cryogenic sleep and his body was warmed to human temperatures. He did not wake and McCoy noticed with his readings he was in deep trouble. He needed to get him back to the _Enterprise_ now. He got the man out of the compartment and onto a hover-sled and beamed back to the _Enterprise _with him. Yet despite all his hard work the man did not wake and they needed answers as to why he was out here in the first place. Kirk called a meeting in the ready room and contacted Starfleet.

"Admiral Gordon here." A tall dark man in gold shirt said as soon as he came on. "Hello Jim what can I do for you?"

"We found a ship out here." Kirk said and told him everything that they had found. "One of the compartments that held one of these people cycled on but the man has not woke up."

"You want to wake up more that it?" Gordon said. "If I say no I know you will anyway."

"So that a yes?" Kirk said.

"Yea, just be careful, these people could be very dangerous." Gordon warned him.

"Yes sir, Kirk out."

He went back to sickbay but McCoy did not have any good news for him and so Kirk headed back to the sleeper ship with Spock and McGivers. They walked through the ship and Kirk saw the perfect one to wake up. He was a young man with blond hair and lightly tanned skin and he looked less threatening than the others. With help from a young engineer the man was taken out of his cryogenic sleep and taken to the _Enterprise_. Later that day the young man woke scared out of his mind.

"Easy son, you are safe." McCoy said to him.

"Where am I?" He asked. "Who are you?"

"I am doctor McCoy, this is the starship USS _Enterprise_." McCoy said. "Who are you?"

"Joachim, I go by Joachim." The young man said looking more fearful as Kirk came into the room. "You are not, not Eugenics?"

"No, you are safe." Kirk said puzzled by this man's reactions. "The year is 2267AD, and you are far from earth."

"New start, a new start they promised us that."

Before Kirk could get anymore out of the boy Joachim fell asleep too tired to stay awake at this time. Kirk had time to speak to him and would let him rest, McCoy would be most unhappy if he did not. This man was going to turn history on its head when McGivers talked to him and found out just what history was stored on the SS _Botany Bay_.


	2. Chapter 2

Chapter Two:

Joachim turned out to be a gentle kind man that everyone liked at once. He was solemn and reserved and there was a haunted look to his eyes, eyes that had seen too much and endured to much in his young life. He was surprised to be asked to dine with the captain and took this honor humbly wishing his commander was the one here not him. Still Kahn had not woke and was still in a coma. Joachim was impressed with the food, it was the best earth dishes on a starship no less!

"Thank you sir for this honor." Joachim said sipping the deep red wine.

"It is not everyday we get to meet someone from history." Kirk said.

"I have read what the history records say of my people." Joachim said a flicker of sadness coming over his face. "I did not expect any different."

"Indeed, you believe the records and incorrect?" Spock asked.

"Yea, well they are." Joachim said. "If I could go to the ship sirs there are records there."

"I am sorry but I cannot allow that." Kirk said. "You must understand the situation we are in."

"Yes sir, I think I do." Joachim said. "I understand why you must have a guard on me and why I am watched as I am."

"Where were you headed?" McCoy asked Joachim.

"The outer stars, forgive me, my commander he knows more of this." Joachim said. "Though I doubt he was told anything either."

The meal went on and Joachim learned much of this era of time. Earth peoples had formed with other races a Federation of worlds that had to main enemies, the Romulans and Klingons. It seemed very few things changed though Joachim dared not say anything about that. He went back to the rooms he was staying in and settled in to read. He looked up as the door opened and Marta McGivers came into the room. She was all sweetness but a suspicion about her formed in Joachim's mind he brushed it away as he was being far too paranoid for his own good.

"Hello." He said getting up and gesturing to a seat. "What can I do for you?"

"I just wanted to see you in person, reading about people like you then seeing you." McGivers said smiling at him.

"People from history can be different in person." Joachim said smiling at her.

"I-I want to help you." She said. "I don't believe the captain is um right in how he is treating you."

"You?" Joachim, "you would help me?"

"Yes." She said.

"In anything, you would help me in anything?" Joachim said his light eyes flashing.

"Yes, please I know you are powerful."

"Get me back to my ship." Joachim said.

"Yes Joachim." McGivers said smiling at him.

She left his quarters and smiled and the guard who smiled back before she knocked him out and drug him into Joachim's quarters. She lead him out and down to the transporter room where she took out the transportation chief. She set the coordinates to the Botany Bay and stepped on the platform with Joachim. They beamed over to the other ship fairly quickly and Joachim headed for the main room he knew what he needed was located.

"Are you not going to wake your people?" McGivers said.

"Instructions are on the sides of the containers." Joachim said busy with the computer. "I will join you in a minute."

"We have to hurry, the captain will come soon." McGivers said.

Joachim found the files he was looking for and began to work feverishly on decoding the files and uploading them. Finally done he walked out to where he saw several of his trusted friends already awake and in far better shape than he had been. Soon they were dressed and ready to beam back to the Enterprise. Captain Kirk right about now would not know what would have hit him as right about now he was no longer in control.

"We have a starship." Joachim said to his fellow solders. "We can go wherever we want now."

"What of Eugenics?" One of the other solders asked.

"Gone, they are all gone." Joachim said. "We won."

"So we are truly free."

"Yes, and all thanks to this young lady." Joachim said looking over at McGivers. "We are going to use an energy transporter straight to the starship."

"Then we find our own world?"

"Yes, our own world to be free on."

The seventy men and women were beamed to the Enterprise in several waves. Finally they were all on board and ready to do whatever Joachim had planned. Joachim had McGivers leave them for a time while he went over his plans with his solders. Kahn would be so proud of him for his cunning. Soon they would all be free with their own world to call home and the galaxy would know the true power of these super solders…


	3. Chapter 3

Chapter Three:

Joachim knew he had to wake his commander, everything hinged on this. Without him the truth would never get out and he was in no position to do this all himself. He was surprised at how lightly guarded the ship was to him. It was so easy to walk through the ship to sick bay and meet very little resistance. He entered and McCoy turned to speak to him but was brushed aside by two of the other super solders. He walked to where Khan was still sleeping and took out a needle and syringe and injected Khan in the neck. Almost at once Khan woke and looked up at Joachim then around the room he was in.

"Sir we do not have much time." Joachim said.  
"Where are we?" Khan asked.  
"On a starship." Joachim said.  
"Eugenics?" Khan asked.  
"No the crew is not, they don't know about us sir." Joachim said. "All but one sir, she has the mark, I designed a device to check for the mark and she has it."  
"What is the year?" Khan demanded.  
"2267AD sir." Joachim said.  
"You think we can trust these people?" Khan said looking keenly at Joachim.  
"Yes sir, look if they know the truth I feel they would use it to help us, not harm us." Joachim said. "However I did wake up the others and we have taken the ship for now."  
"Any deaths?" Khan asked.  
"No, we have not killed anyone, as if we need start out that way."

Joachim helped Khan up who was still a bit weak but recovering fast. He got dressed in his uniform, gray/green fatigues, black armor and boots and weapons. Joachim was dressed the same way now and Khan had the commander insignia on his uniform. Khan sat down for a moment and read quickly through the histories that this civilization had on them. Lies, it was all lies and he was angered by this. As always they were betrayed and he would make those who did this pay.

"Sir I uploaded the history files to their databases." Joachim said and seeing a flicker of anger on Khan's face. "Sir at least if they look at them and do nothing we will be justified in what we do."  
"Very well, who is the commander of this ship?"  
"Captain James Kirk sir." Joachim said.  
"I see, I wish to speak to him." Khan said.

On the bridge captain Kirk was not very happy, his ship had just been taken over by a bunch of thugs from the twentieth century. He was really thinking of not going to meet with the newly awake Khan. Still he was the captain and he had to try to save his ship if he could. He stood up straightened his tunic and walked off the bridge with Spock by his side to the recreation room. He was not happy to see the Joachim and Khan clad as it were for war.

"Why did you take my ship?" Kirk demanded.  
"We felt it was the only way." Khan said. "I am not sure if we can trust you."  
"So you take my ship?" Kirk said highly upset.  
"All I ask is you look at the data we have." Khan said.  
"If I say no?" Kirk said.  
"Then we take your ship." Khan said. "I do not want to kill you but I will if I have to in order to gain my people's freedom."  
"It would do no harm to look at their files captain." Spock said.  
Kirk knew he did not have a choice, to save his crew he had to do as he was asked, more like ordered to. He sat down at the computer and began to read the files that had been downloaded from the Botany Bay…


	4. Chapter 4

Chapter Four:

Kirk sat back stunned at what he had learned from the files. Spock looked thoughtful or as close to it as he could. The files, the raw data complied compressed to easy to read forms, the manipulation by the Eugenics who had done all they could to change human history and indeed human DNA to their specifications, to hell with what GOD had in mind for the human race. What was more with the family trees of the Eugenics spread out before him he could see that McGivers related to the Eugenics and if not one of them she was a prime suspect.

"Is my lieutenant one of these Eugenics?" Kirk asked Khan.  
"Yes she is, a simple test will prove it, she has the mark, as Joachim has seen it." Khan said.  
"I can see at times into the infrared rage if I concentrate." Joachim said. "I don't do it often it gives me a headache."  
"Joachim." Khan warned the younger man getting him back on track.  
"Right, well the mark only shows up under infrared light, it is just below the right ear." Joachim said.  
"It is up to you now captain." Khan said sitting back looking at Kirk keenly. "Your move."  
"Fine, I will contact Starfleet, Admiral Thomas Gordon can be trusted." Kirk said.  
"Very well, but we stay here." Khan said.

Kirk called admiral Gordon and by the strained look on his face Gordon knew something was up. Kirk relayed what he had just learned and sent the files to Gordon and waited while Gordon read the files. Finally he looked up and sighed, he really did not need this today. He never did like conspiracies and here was one staring him right in the face.

"I am going to set a conference." Gordon said. "In the meantime I want you to arrest that lieutenant of yours now."  
"What of us?" Khan said. "What will you do with us?"  
"Give back the Enterprise to captain Kirk, I promise no charge will be brought, with what I have seen you were acting only on self preservation."  
"I will do that, however my people stay armed." Khan said. "No negotiations on that."  
"Very well." Gordon said looking very strained.

Kirk found McGivers talking with one of the survivors of the Botany Bay and he saw her go white as he arrested her. He wanted to know why she had done what she had, she was not trying to free the peoples of the Botany Bay but destroy them and he wanted to know why. That was why he took her back to the conference room where she trembled at seeing Spock. She knew what he could do but she was not going down without a fight.

"Why did you betray Starfleet?" Kirk asked her. "You can tell me or Mr. Spock will find out for us."  
"They are impure." McGivers said. "For centuries we have waited to destroy them, they are impure."  
"We are what we are because of your kind!" Khan snarled wishing to strike her.  
"So your people have waited for centuries to destroy them, are you trying to create a superhuman race?"  
"No." McGivers said.  
"What then?" Kirk asked.  
"The gamma quadrant." McGivers said.  
"What of the gamma quadrant?" Spock said. "None in recent history has traveled there."  
"The Dominion sees all, if these super humans survive the Dominion will destroy all."  
"An excuse." Khan said. "You speak of vague things to justify hurting and harming and killing us!"  
"The prophecy speaks if this!" McGivers said.  
"Prophecies of a madman no doubt." Joachim said.  
"So this goes further than earth." Spock said. "Fascinating."

At this moment Gordon called back with the news, the peoples of the Botany Bay were to be officially declared dead. However in deep secrecy they would get a sector of their own to live in. All that had to be done was to come to a neutral star base and sign the treaty that would make this official. Khan spoke to his people and agreed to this, it was his chance to save his people and help them gain a new world…


	5. Chapter 5

Chapter Five:

Khan sat back and rubbed his eyes realizing he needed to get sleep. He had been at this for days now, going through the earth histories of the past few centuries trying to make since of why things had happened the way they had. He knew God had a hand in allowing them to even survive all they had. Truly there was a reason he was alive and here now and as he looked he grew frustrated. He got up and drew his long red robe tighter around himself and walked out to his balcony and looked over the small city below.

This world he was on was a good world, fertile and loving to him and his people. The treaties had been signed and officially the Botany Bay had been found filled with dead people. They now had this sector of fifty habitable systems to grown and live on. So far this one world was being colonized as people wishing for a new life outside the Federation. This city was a start, a full 50,000 American Indians were here and their influence was felt strongly here.

Farming was done mostly by machine and so the majority of the people had spent their time building this city. It was built of green tinged buildings with red tiled roofs. The city reminded Khan of pictures of ancient Rome he had seen growing up. Khan turned as Joachim came into the room and walked over to Khan.

"You should rest." Joachim said.  
"I know it is in here somewhere." Khan said. "Why would Eugenics wish us dead even after all this time? It does not make since, after all they engineered us."  
"Against God's will." Joachim said.  
"Yet we live, God is not upset with us, we did not ask to be genetically engineered." Khan added understanding what Joachim said. "How go the elections?"  
"Very well, so far the people are voting for the constitution government."

Khan really did not want power, that was not his aim in life to be a dictator, he had fought against those who had wished to destroy the world. The lies that had been spread in history that he was one of the dictators he had fought against. He would show them, this election would prove he was not that kind of man. It was this reason he had taken the constitution of the United States of America and now brought this to a vote of the people to see if they would accept this as their law. So far they seemed to want it.

"More peoples are wishing to live here." Joachim said.  
"Let them come, as long as they are willing to work hard and abide the laws set up." Khan said. "We are not Federation and we will not be, they must realize that."  
"Understood." Joachim said. "That is why you banned replication technology."  
"It is a good idea on paper, but it keeps the human mind from fully developing fully. How can a human fully develop if he has all he needs handed to him and does not have to work for it?"  
"Good point." Joachim said. "But you need to rest sir."  
"Very well, in the morning I will come to you and we can work on this more."

Khan went to his bedchamber and slept well that night, he woke early, went for a run and a swim, then had a large breakfast. He started back in on his tedious work and slowed down as he came across several files that he carefully looked over. He picked them up and carried them to where he kept the histories he had taken from Earth and compared them with those he had found. So far Eugenics had been a fully Earth based group, but in 1947 something changed. He looked from one file to the other and it hit him why Eugenics wanted his people dead.

"I found it!" Khan said as soon as he found Joachim. "Look it is clearly here!"  
"The crash, that would explain much." Joachim said.  
"There is no prophecy." Khan said. "It is an alien life force that crashed on earth and no doubt is still alive."  
"We need to warn Kirk." Joachim said.  
"Agreed, he has earned my trust." Khan said. "Is he not an Admiral now?"  
"Yes, it has been a few years since the five year mission ended, no doubt the years have been kind to him." Joachim said.  
"They have not been to me." Khan said holding a hand up to his mostly silver hair.  
"Thought that was because of your wife and children sir." Joachim said.  
"You have to get married" Khan said, "a wife and children changes you, makes life that much better."  
"You know me, the eternal bachelor." Joachim said grinning. "So you wish me to call Kirk?"  
"Yes, he needs to know what we are up against."

Joachim did exactly that on the secure channel he had to the Federation. Hopefully Kirk would still be willing to help even after all these years. They needed to stop what was happening if the Galaxy was to survive at all…


	6. Chapter 6

Chapter Six:

Khan stood on the observation deck of the Enterprise feeling strange being back here. So much had changed, he had, the Admiral standing by him, but the Enterprise was the same. He looked over at the Reliant that was here watching the experimental project under way. Khan had come here under cover of wanting to see what the Genesis Project was all about. In fact he was here because he needed answers. He looked over at Kirk and noticed that he was thicker in the waist and a bit older but he still was strong and spry at his age.

"Not sure about this." Kirk said looking out at what was about to happen with the barren world below. "Not sure this should be done."  
"At least you and I agree with that old friend." Khan said.  
"Still it could be, interesting if it really does work." Kirk said.

The men were joined by others from the crew, captain Spock, commander McCoy and commander Scotty were a few that joined them to watch the Genesis project unfold. At a signal the device was detonated over the planet. As the ships were out of range of any damage they could watch this in peace. This was not like Terra-forming a world, this was creating a whole new world of life. Something a few had a hard time with, many were hoping it did not work, and that was unfair, the scientist, Carol Marcus and her son David Marcus had put a lot into this.

"Seems to be working right on schedule." Kirk said watching as oceans were formed and landmasses separated by water.  
"I do not agree with this." Khan said. "It goes against God."  
"I could not agree more." McCoy said standing by him.

Finally when there was not much more to see Kirk lead the hooded figure of Khan to his ready room. There Spock waited with them and it was clear that he had something for him. Khan sat down and called up the files onto his screen. He found himself looking at several photos of different people. But as he looked he saw tell-tale signs. He started to over lap the photos and it became clear this was the same person.

"This is the same person." Khan said.  
"All from different times." Spock said. "McGivers has been most helpful."  
"Nearly fifteen years in isolation can do that to a person." Kirk said.  
"So if this is the same person that means they can shape shift." Khan said.  
"But there is always that tell tale thing on them, something deliberate." Spock said.  
"The sign of the new prophet." Kirk said.  
'That means there is one more prophet out there." Khan said. "No a false prophet, if this is a shape shifter, is there a way to contain one?"  
"Yes I believe there is." Kirk said.  
"Good, now we just need to find it." Khan said.

It took two years and in that time Kirk lost a son he never knew he had to the Klingons. The Enterprise was destroyed in battle and Kirk had gone back in time to save Earth. Finally Khan was able to meet the shape shifter face-to face. The only question he had was why, why had this creature done what it had? He was surprised at how it looked, tall with a face that looked like it was badly molded out of putty but with eyes as alive and feral as could be.

"Can I ask why you did what you did?" Khan asked.  
"I was doing what the Dominion would wish." It said. "But humans cannot be turned to our needs."  
"What does that mean? Oh of course I am a failure to you, it all makes since to me now. You try and thwart God and make slaves to do your bidding." Khan said. "I will see you die, I will find out how and before I leave this earth you will perish for your great evil."  
"Do your worse human!" It spat. "I have lived five hundred years, you cannot kill me!"  
"I will find out how shape shifter." Khan said. "You have my word on that."

The creature hit the seamless clear structure it was trapped in with frustration. It knew it was trapped and could not get out. Khan would keep his word, but for now he had Eugenics to deal with. With a small force of men he over threw them and liberated their slaves, genetically engineered super solders. His heart ached as most were mere children and had never known a mother or father. He would change that, they would now have family and live with his people on his world. Freedom never had felt so good to him than now, liberating what he called his people.


	7. Chapter 7

Chapter Seven:

Khan had come to the end of his life, he was dying and he had his family around him. Life could have turned out far worse for him but he had not. He had been stunned when Admiral Kirk had died trying to rescue a ship-full of El-Aurians that had escaped the Borg when they had tried assimilate their home world and destroyed it instead. Many of the El-Aurians had come to live in American Space as it was called now and they were a welcome addition. New races were found too, Cardassians and Bejorans were found and tentative talks were in place with the two species.

Khan looked around at his family gathered around his bed and smiled. He was dying of advanced cancer, there was nothing that could be done. However he was not in any pain, no the pain drugs that were out there kept his body free of pain and his mind clear. He did not fear dying, he knew it was part of life and he would be in heaven before the day was out. His dear wife, Rose sat by his side, her sweet lined face was framed by her white hair and she looked beautiful to him. He had lived thirty years after Kirk had died and he missed the man though he had not spent much time with him. He had given him a second chance at life and for that he was grateful.

"Do you need anything?" Rose asked him.  
"No, I have all you and I am content." Khan said looking around at the generations here.  
"I am not sure I am ready to live with out you yet sir." Joachim said kneeling by the beside of his mentor, commander and now father-in-law. "You have always been there for me."  
"I still will be, in your children, your grandchildren and in these people who come to this part of space to live and prosper."

Khan looked around at his five children, two boys, three girls and his twenty grandchildren and forty great grandchildren. All he had ever wanted was family and with the grace of God he mused he got it. He smiled and lay back on the bed and smiled and closed his eyes. His breathing slowed down and mercifully, peacefully he died in his sleep. His wife wept quietly by his side her grief was deep but at least her husband had not died in pain or in vain.

Across the sector the peoples remembered a good charismatic man who had lead this sector to great riches and prosperity. As the years passed the memory of Khan did not, a young man named Jean Luc Picard married one of his great granddaughters, left Starfleet to raise a family then took a commission as captain on the USS Enterprise D. The Bejorans and Cardassians very nearly went to war and it was the American sector that kept that war from ever happening.

The wormhole was found in the Bejoran system and a new star base was built and the American sector that now included the warlike Cardassians and the peaceful spiritual Bejorans. The Bejorans in a token of good will toward the Federation allowed them to share the star base that was renamed Deep Space 9. Then there was the troublesome separatist group called the Marquis that did not want to be part of the Federation or the American sector and declared war on both. The USS Voyager was lost in the delta sector when chasing a Marquis ship.

War did come to the American Sector, the Dominion in the Gamma Quadrant declared war on the Alpha Quadrant. They were unaware of how strong the alliance was between the Bejoran and Cardassian peoples and their fateful mistake of trying to divide them failed. The Dominion was crushed and that only left the Borg to fight off. All this would never have come to pass if not for a change that took place many, many years ago. It was all due to a small group of humans from late twentieth century earth that just wanted freedom and managed through hard work to create a new sector of wealth and prosperity.

The End.


End file.
